Documentation read from 04/17/2019 22:07:28 version of /vol/public-pseed/FIGdisk/FIG/bin/svr_taxonomically_related_genomes.



    svr_taxonomically_related_genomes [-c] [-d depth] < genome_ids > expanded_genome_ids

Get a list of genomes that are taxonomically related to the input genomes.


Usage: svr_taxonomically_related_genomes [-c] [-d depth] < genome_ids > expanded_genome_ids

       -c  turn on caching; fetch taxonomy data over sapling only once
       -d  taxonomy level  (D = 7, species)
       -t  show taxonomy hierarchy of the input genomes

       If genome IDs are found in the command line, STDIN is not read.


       1. Get all Bacillus genomes

          svr_taxonomically_related_genomes -d 6 224308.1 

       2. Get all Escherichia coli genomes using cached taxonomy info

          svr_taxonomically_related_genomes -d -1 -c -t 83333.1

Command-Line options


Turn on caching; fetch taxonomy data over sapling only once.

-d depth (D = 7)

Taxonomy level. (1: Kindom, 2: Phylum, 3: Class, 4: Order, 5: Family, 6: Genus, 7: Species, 8: Strain)

Use negative numbers to go up from the highest taxonomy level.


Show taxonomy hierarchy of the query genomes.


The input is a list of genome IDs supplied in the command line or read from STDIN.


The output is a list of related genome IDs written to STDOUT.